Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

ScienceMatters@Berkeley April 2007

As usually the latest issue of ScienceMatters@Berkeley includes several intersting articles including, The Protein Machine by Kathleen M. Wong

A large percentage of known antibiotics target bacterial ribosomes, including tetracycline, erythromycin, and streptomycin. Many of these antibiotics have been isolated from microbes themselves. “It’s a byproduct of the chemical warfare that’s been going on among bacteria for hundreds of millions of years,” Cate says. “We want to understand how these natural products inhibit translation. Then, based on what we understand about the ribosome mechanism, we should be able to come up with new ways to stop bacterial translation based on the old compounds.”

Self-Tuning Genes:

Researchers such as UC Berkeley’s Adam Arkin have found that regulatory feedback is associated with chance fluctuations in mRNA or protein levels—a phenomenon called expression noise. “Even though they’re all genetically identical, and grown under the same conditions, yeast clones don’t express certain proteins at exactly the same level,” Brem says. “Some genes are noisier than others. That makes people think the cell is actively tuning the distribution around an expression level set by the regulatory network.” Noise may ensure that a few individuals can handle abrupt changes in their environment. In other words, if a colony is suddenly assaulted by toxic chemicals or high heat, a few individuals will already have expression levels suited to those conditions.

Software Patents – Bad Idea

MIT League for Programming Freedom on Software Patents, including: Why Patents Are Bad for Software, No Patents on Ideas by Thomas Jefferson and letter from Donald E. Knuth to the U.S. Patent Office

In the period 1945-1980, it was generally believed that patent law did not pertain to software. However, it now appears that some people have received patents for algorithms of practical importance–e.g., Lempel-Ziv compression and RSA public key encryption–and are now legally preventing other programmers from using these algorithms.

This is a serious change from the previous policy under which the computer revolution became possible, and I fear this change will be harmful for society. It certainly would have had a profoundly negative effect on my own work: For example, I developed software called TeX that is now used to produce more than 90% of all books and journals in mathematics and physics and to produce hundreds of thousands of technical reports in all scientific disciplines. If software patents had been commonplace in 1980, I would not have been able to create such a system, nor would I probably have ever thought of doing it, nor can I imagine anyone else doing so.

Math and Nature

Can’t Knock It Down:

Give mathematicians such a toy, and they’re liable to turn it into a math problem.

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Next, the pair began to investigate whether all three-dimensional shapes have at least two stable and two unstable balance points. They tried to generalize their two-dimensional proof to higher dimensions, but it didn’t hold up. Therefore, it seemed possible that a self-righting three-dimensional object could exist. Such a shape would have only one stable and one unstable balance point.
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Once the pair had built their Once the pair had built their self-righting object, they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back., they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back.
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The mathematicians still face an unanswered question. The self-righting objects they’ve found have been smooth and curvy. They wonder if it’s possible to create a self-righting polyhedral object, which would have flat sides. They think it is probably possible, but they haven’t yet managed to find such an object. So, they are offering a prize to the first person to find one: $10,000, divided by the number of sides of the polyhedron.

Stanford Center for Professional Development Seminars

Free, Stanford Center for Professional Development seminar webcasts

During the autumn, winter and spring quarters, the Stanford Center for Professional Development makes it possible for the public to view a series of thought-provoking seminars on a broad range of topics. The weekly seminars feature presentations by distinguished Stanford faculty, senior researchers and industry experts. They are available for viewing online via streaming video.
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Bioengineering and Biodesign Forum
Statistics for Research
Human-Computer Interaction
Entrepreneurship in Asian High-Tech Industries
Design and Manufacturing Forum
Lessons in Decision Making
Entrepreneurial Thought Leaders Seminar
Broadening the Appeal of Engineering to Women

Via: Stanford Engineering Research Seminars

And Now for Something Completely Different

Macavity the cat

Too cool. Mystery cat takes regular bus to the shops:

The cat was nicknamed Macavity after the mystery cat in T.S Elliot’s poem. He gets on the bus in front of a row of 1950s semi-detached houses and jumps off at a row of shops down the road which include a fish and chip shop.
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Driver Bill Khunkhun, 49, who first saw the cat jumping from the bus in January, said: “It is really odd, the first time I saw the cat jumping off the bus with a group of passengers. I hadn’t seen it get on which was a bit confusing. “The next day I pulled up on Churchill Road to let a couple of passengers on. As soon as I opened the doors the cat ran towards the bus, jumped on and ran under one of the seats, I don’t think any of the passengers noticed. “Because I had seen it jump off the day before I carried on driving and sure enough when I stopped just down the road he jumped off – I don’t know why he would catch the bus but he seems to like it. I told some of the other drivers on this route and they have seen him too.”

Here is T.S. Eliot’s poem:

Macavity’s a Mystery Cat: he’s called the Hidden Paw-
For he’s the master criminal who can defy the Law.
He’s the bafflement of Scotland Yard, the Flying Squad’s despair:
For when they reach the scene of crime-Macavity’s not there!

Macavity, Macavity, there’s no one like Macavity,
He’s broken every human law, he breaks the law of gravity.
His powers of levitation would make a fakir stare,
And when you reach the scene of crime-Macavity’s not there!
You may seek him in the basement, you may look up in the air-
But I tell you once and once again, Macavity’s not there!
Continue reading →

Changing the Circadian Clock with the Seasons

Changing the Circadian Clock with the Seasons:

The findings – gleaned from work on the fruit fly Drosophila – have broad implications for understanding how innate behaviors such as mating, migrating, and hibernating are stimulated by environmental cues. Dan Stoleru, the lead author of the Cell paper and a postdoctoral fellow in Rosbash’s laboratory at Brandeis University, adds that the study reveals insights into possible causes of seasonal depression as well as other forms of mood disorders that respond to light therapy.
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Rosbash is a leader in the field of circadian research. For the past 25 years he has been defining the machinery that underlies the nearly universal pattern of circadian rhythms in insects, animals, and humans. He employs the tools of Drosophila genetics to understand how the circadian clock ticks and which master neural circuits underlie circadian activity patterns.

Lego Autopilot Project Update

An update to, The sub-$1,000 UAV Project from Chris Anderson – Lego Autopilot is Working!:

Our summer project is to create a sub-$1,000 UAV as a proof-of-concept for a drone competition for kids. This weekend we passed a major milestone with a successful ground test of the key elements. The video below shows the prototype working.

We’d initially intended to do all the autopilot functions in Lego, but the gyro programming turned out to be beyond our abilities. So we switched to a commercial stabilization unit to keep the plane level and just use the Lego Mindstorms for waypoint navigation.

Very cool.

Young Scientists Design Open-Source Program at NASA

Young Scientists Design Open-Source Program at NASA:

The program was launched quietly last year under NASA’s CoLab entrepreneur outreach program, created by Robert Schingler, 28, and Jessy Cowan-Sharp, 25, of NASA’s Ames Research Center in Mountain View, California. Members of the CosmosCode group have been meeting in Second Life and will open the program to the public in the coming weeks, organizers said.

“NASA is recognizing the value of free and open-source software in other sectors,” said Cowan-Sharp, a contractor at NASA Ames in Mountain View, California. “CosmosCode is going one step further by allowing NASA scientists to begin a software project in the public domain, leveraging the true value of open-source software by creating an active community of volunteers.”

CosmosCode is indicative of a larger shift at NASA toward openness and transparency — things for which complex and bureaucratic government labs are not known. The software project is part of CoLab, an effort to invite the public to help NASA scientists with various engineering problems. NASA is also digging into its files from previous missions and releasing code that until now remained behind closed doors. Together, these projects are creating a sort of SourceForge for space.

Related: CosmosCode – Second Life Intern – NASA CoLab

Math’s Architect of Beauty

Math’s Architect of Beauty – How Terence Tao’s quest for elegance earned him a Fields Medal and a MacArthur Fellowship

The prime numbers do obey some simple patterns—for instance, all primes but 2 are odd numbers. The great achievement of the Green-Tao theorem is its use of subtle and novel methods of harmonic analysis (very much indebted to the work of 2002 Fields Medalist Timothy Gowers) to show that these simple patterns are essentially the only structure the primes possess. Beyond these basic structures, the primes look random—they are, in a sense, all noise and no music.

Related: Terence Tao – math related posts

Bedbugs Are Back

Bedbugs bounce back: Outbreaks in all 50 states by Meredith May:

Pest control companies nationwide reported a 71 percent increase in bedbug calls between 2000 and 2005. Left alone, a few bedbugs can create a colony of thousands within weeks. “We never treated bedbugs until 2002. Now we have a dedicated bedbug crew working on this every day,” said Luis Agurto, president of Pestec in San Francisco.

Agurto’s arsenal includes a vacuum, steam heat to cook the bedbug eggs and targeted spraying of insecticides. It takes three, eight-hour visits and about $500 to $750 to exterminate one room. A whole house would cost closer to $5,000.
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Nearly all exterminators use pyrethroids, which are a synthetic version of pyrethrum, the substance found in chrysanthemum flowers. But last fall, at the University of Kentucky, some of the nation’s best bedbug researchers delivered some sobering news — while they could kill bedbugs born in the lab with pyrethroids, four groups of adult bedbugs brought in from the outside were unaffected.

University extension offices often have the soundest scientific information – try the links below for more details.